September 22, 2019  |  

The maize W22 genome provides a foundation for functional genomics and transposon biology.

Authors: Springer, Nathan M and Anderson, Sarah N and Andorf, Carson M and Ahern, Kevin R and Bai, Fang and Barad, Omer and Barbazuk, W Brad and Bass, Hank W and Baruch, Kobi and Ben-Zvi, Gil and Buckler, Edward S and Bukowski, Robert and Campbell, Michael S and Cannon, Ethalinda K S and Chomet, Paul and Dawe, R Kelly and Davenport, Ruth and Dooner, Hugo K and Du, Limei He and Du, Chunguang and Easterling, Katherine A and Gault, Christine and Guan, Jiahn-Chou and Hunter, Charles T and Jander, Georg and Jiao, Yinping and Koch, Karen E and Kol, Guy and Köllner, Tobias G and Kudo, Toru and Li, Qing and Lu, Fei and Mayfield-Jones, Dustin and Mei, Wenbin and McCarty, Donald R and Noshay, Jaclyn M and Portwood, John L and Ronen, Gil and Settles, A Mark and Shem-Tov, Doron and Shi, Jinghua and Soifer, Ilya and Stein, Joshua C and Stitzer, Michelle C and Suzuki, Masaharu and Vera, Daniel L and Vollbrecht, Erik and Vrebalov, Julia T and Ware, Doreen and Wei, Sharon and Wimalanathan, Kokulapalan and Woodhouse, Margaret R and Xiong, Wenwei and Brutnell, Thomas P

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

Journal: Nature genetics
DOI: 10.1038/s41588-018-0158-0
Year: 2018

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